Comments (2)
Dear @AbhishakeL,
probably the error is due to empty sequences in the input fastq files. The version of VSEARCH integrated in micca does not allow input files in FASTQ format to have empty sequences (see torognes/vsearch#175). For now the solution is to discard the empty sequences (e.g. using cutadapt) before merging.
Let me know if it works,
Davide
from micca.
The problem was that one of the sequence files was buggy. However the error report gives no clue as to which file is that. Initially I thought the line number here refers to the line number of the merged.fastq file, which is not the case. So i grep -ed through the entire merged.fastq to find out which sample name was missing.
So is it possible to add the file name in the error report?
from micca.
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